Comparison of protocols for pulsed-field gel electrophoresis of Clostridia

Genotyping of bacterial strains via pulsed-field gel electrophoresis has to be considered an important tool for epidemiological investigations in food hygiene as well as in other areas. Yet, a major disadvantage of this metho d is its long duration. Therefore, rapid procedures for DNA isolation and r estriction are being sought. One such protocol was modified and further sho rtened to two days. This short protocol was used for macrorestriction analy sis of 34 strains of 25 different Clostridium species. Parallel analyses we re performed using a conventional 5-day protocol in order to compare the lo ng and the short method by running the DNA samples obtained via both protoc ols on the same gel. In the case of nine strains, none of the two methods y ielded satisfactory results, whereas for three strains the long protocol pr oved to be preferable to the short one. Comparable results were obtained us ing both methods in the case of 22 strains belonging to 17 different Clostr idium species.